[R-SIG-Mac] gfortran: command not found

Spencer Graves @pencer@gr@ve@ @end|ng |rom prod@y@e@com
Thu Jul 6 21:29:51 CEST 2023 

Hi, Peter et al.:


On 7/6/23 1:15 PM, Peter Dalgaard wrote:
> I think the cleanest way is to diddle the /etc/paths.d structure. I have
> 
> PeterDaardsiMac:R pd$ ls /etc/paths.d
> 40-XQuartz	R		TeX		clang8		gfortran
> PeterDaardsiMac:R pd$ cat /etc/paths.d/gfortran
> /usr/local/gfortran/bin
> PeterDaardsiMac:R pd$ cat /etc/paths
> /usr/local/bin
> /usr/bin
> /bin
> /usr/sbin
> /sbin
> 
> and the latter would want to be /opt/gfortran/bin for 12.2 (I still have 8.2 for now).


	  I could not figure out how "to diddle the /etc/paths.d structure", 
but I was successful by appending "/opt/gfortran/bin" to etc/paths using 
"sudo vi etc/paths".  It didn't work immediately nor after I exited and 
restarted Terminal, but it did after I rebooted.


	  There's till a lot I do not understand about this. 
readLines('/etc/paths') now returns a character vector of length 8, with 
the last string being the one I appended. Meanwhile, "echo $PATH" at a 
prompt returned a path with 13 components with "/opt/gfortran/bin" being 
number 11, and 'Sys.getenv("PATH")' returned a path with 18 components, 
with "/opt/gfortran/bin" being number 12.


	  Anyway, thanks again to Simon and Peter.


	  Best Wishes,
	  Spencer Graves

> 
> Two things to note:
> 
> 1. The directories in paths.d/* are added to those in /etc/paths in alphabetical order, so careful with older versions in /usr/local/bin.
> 
> 2. You (probably) need to logout and back in for the changes to take effect in your Terminal windows.
> 
> Alternatively, you can twiddle the shell startup files (~/.profile /etc/profile /etc/bashrc ....) directly. The trouble I have with that, is that I never feel sure that I am doing it in the right place.
> 
> - Peter D.
> 
>> On 6 Jul 2023, at 19:58 , Spencer Graves <spencer.graves using prodsyse.com> wrote:
>>
>> 1.  I need to apologize to Simon:  I failed to see his reply to the original post.  Then I found the instructions and installed gfortran-12.2-universal.pkg, as indicated there, but it still didn't work.
>>
>>
>> 2.  I'm not finding clear instructions on how to update the path on macOS 11.7.8, which is the latest version available for my 2014 MacBook Pro with a 2.8 GHz Quad-Core Intel Core i7.  I found several pages with differing instructions.  I found one in "support.apple.com" that recommended something that didn't work.[2]
>>
>>
>> 	  Further suggestions?
>> 	
>>
>> 	  Thanks again very much.
>> 	  Spencer Graves
>>
>>
>> [2] "support.apple.com" recommended "PATH=/bin:/sbin:/user/bin:/user/sbin:/system/Library/ export PATH", then "env".  I did "env" to get the current path, than appended ":/opt/gfortran/bin" to that and executed the revised "PATH=...:/opt/gfortran/bin export PATH".  However, when I checked with "env" again, the change was not displayed.  I rebooted with the same result.
>>
>>
>> https://support.apple.com/guide/terminal/use-environment-variables-apd382cc5fa-4f58-4449-b20a-41c53c006f8f/mac
>>
>>
>> On 7/6/23 11:01 AM, Simon Urbanek wrote:
>>> AFACT he didn't say so, there was no response, just double-posting of the same question after is was answered.
>>> The installer says:
>>> The resulting compiler will live in /opt/gfortran and can be called with
>>> /opt/gfortran/bin/gfortran
>>> so it's advisable to have /opt/gfortran/bin on the PATH.
>>> (Side note: the arm64 build of R uses the full path, but some people have been objecting to that since they wanted to use other compilers for the legacy Intel builds, but as I suspected that causes other issues, so I'll change that for the next release).
>>> Cheers,
>>> Simon
>>>> On Jul 6, 2023, at 11:45 PM, Peter Dalgaard <pdalgd using gmail.com <mailto:pdalgd using gmail.com>> wrote:
>>>>
>>>> AFAICT, Spencer followed the implied instructions and it still didn't work.
>>>>
>>>> There may also be a PATH issue when upgrading to 4.3.x, /usr/local -> /opt/R/<arch> Does gfortran 12.2 install to /opt/R/.../bin ?
>>>>
>>>> -pd
>>>>
>>>>> On 6 Jul 2023, at 07:42 , Simon Urbanek <simon.urbanek using r-project.org <mailto:simon.urbanek using r-project.org>> wrote:
>>>>>
>>>>> Already answered to you and on R-pkg-devel [9 mins after you posted there - now more than 5h ago...]:
>>>>>
>>>>> To quote from the page you downloaded R from:
>>>>>
>>>>> This release uses Xcode 14.2/14.3 and GNU Fortran 12.2. If you wish to compile R packages which contain Fortran code, you may need to download the corresponding GNU Fortran compiler from https://mac.R-project.org/tools <https://mac.R-project.org/tools> <https://mac.r-project.org/tools <https://mac.r-project.org/tools>>.
>>>>>
>>>>>
>>>>>
>>>>>> On Jul 6, 2023, at 5:16 PM, Spencer Graves <spencer.graves using prodsyse.com <mailto:spencer.graves using prodsyse.com>> wrote:
>>>>>>
>>>>>> Hello, All:
>>>>>>
>>>>>>
>>>>>>   "R CMD check KFAS" under macOS 11.7.8 (the latest version that will run on my aging Mac) complains "gfortran: command not found".
>>>>>>
>>>>>>
>>>>>>   I just upgraded to R 4.3.1 and installed "gfortran-12.2-universal.pkg" per "https://cran.r-project.org/bin/macosx/tools/<https://cran.r-project.org/bin/macosx/tools/>".  I expected this to solve the problem.  It didn't.
>>>>>>
>>>>>>
>>>>>>   Suggestions?
>>>>>>   Thanks,
>>>>>>   Spencer Graves
>>>>>>
>>>>>>
>>>>>> p.s.  This is my fork of KFAS, available at "https://github.com/sbgraves237/KFAS <https://github.com/sbgraves237/KFAS>".  "sessionInfo()" appears below.
>>>>>>
>>>>>>
>>>>>> ##########
>>>>>>
>>>>>>
>>>>>> sessionInfo()
>>>>>> R version 4.3.1 (2023-06-16)
>>>>>> Platform: x86_64-apple-darwin20 (64-bit)
>>>>>> Running under: macOS Big Sur 11.7.8
>>>>>>
>>>>>> Matrix products: default
>>>>>> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>>>>>> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
>>>>>>
>>>>>> locale:
>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>>>>
>>>>>> time zone: America/Chicago
>>>>>> tzcode source: internal
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] compiler_4.3.1  R6_2.5.1        magrittr_2.0.3  cli_3.6.1
>>>>>> [5] tools_4.3.1     glue_1.6.2      rstudioapi_0.14 roxygen2_7.2.3
>>>>>> [9] xml2_1.3.4      vctrs_0.6.2     stringi_1.7.12  knitr_1.42
>>>>>> [13] xfun_0.39       stringr_1.5.0   lifecycle_1.0.3 rlang_1.1.1
>>>>>> [17] purrr_1.0.1
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
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>>>>
>>>> -- 
>>>> Peter Dalgaard, Professor,
>>>> Center for Statistics, Copenhagen Business School
>>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>>> Phone: (+45)38153501
>>>> Office: A 4.23
>>>> Email: pd.mes using cbs.dk <mailto:pd.mes using cbs.dk>  Priv: PDalgd using gmail.com <mailto:PDalgd using gmail.com>
>

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